Hello all,

I get the following warning when parsing a fasty34 HSP using Bio::Search
and then trying to getting the alignment using get_aln

MSG: In sequence CONTIG residue count gives end value
565.333333333333.  
Overriding value [565] with value 565.333333333333 for
Bio::LocatableSeq::end().
MAEMFKIGDLVWAKMKGFSPWPGLVSNPTKDLKRPTSKKSAQQ/C/VFFLGTNNYAWIEEANIKPYFEYRDRLVKSNKSGAFKDALDAIEEYIKNNGAKFDDPDAEFNRLRESLAEKKESKPKQRKEKRPAHDDNSAKSPKKVRTNSVEADKESVRADSPILSNHSPRKGPASTLLERPTTIVRPLDDSQD
STACK
Bio::LocatableSeq::end /usr/local/share/perl/5.8.8/Bio/LocatableSeq.pm:196
STACK
Bio::LocatableSeq::new /usr/local/share/perl/5.8.8/Bio/LocatableSeq.pm:140
STACK
Bio::Search::HSP::FastaHSP::get_aln /usr/local/share/perl/5.8.8/Bio/Search/HSP/FastaHSP.pm:174

The frameshifts (/ and \ ) are causing this recalculation of length to a
float (which is a bit weird) but is not fatal for my program. Is this
intentional?

My immediate problems is actually the warning message itself - which is
quite annoying if you have hundreds of such sequences... any way to turn
them off sort of commenting out the line at LocatableSeq.pm ?
(redirecting STDERR wouldn't be desirable for a production script).

many thanks
alexie


-- 
Alexie Papanicolaou
Richard ffrench-Constant group
CEC-Biology
Univ. Exeter in Cornwall
Penryn
TR10 9EZ
United Kingdom



